[FieldTrip] fieldtrip Digest, Vol 18, Issue 33

Mon May 21 12:07:02 CEST 2012

Thank you Arjen and Giovanni, and good point Gio, didn't think of that 
before but now that you mention, it's really obvious that that would 
create a difference between the conditions in itself.
I'll go for random then.

Cheers, Vitória

On 21-5-2012 12:00, fieldtrip-request at donders.ru.nl wrote:
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> Today's Topics:
>
>     1. error using ft_databrowser (Inbal Shapira Lots)
>     2. Re: Changing samplingrate for EGI-data (Nathan Weisz)
>     3. Re: equal number of trials across conditions (Stolk, A.)
>     4. Re: equal number of trials across conditions (Gio Piantoni)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 20 May 2012 14:02:58 +0300
> From: Inbal Shapira Lots<inbalots at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] error using ft_databrowser
> Message-ID:
> 	<CALYKD0rS_j-A2uGVejW_=Yqe+av-2tu--uEfwzcPN9b3U=N9eQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello
> I call the function in the following way:
> cfg = [];
> cfg.dataset=fileName;
> cfg.trialdef.beginning=0.1;
> cfg.trialdef.end=0.2;
> cfg.trialfun='trialfun_raw';
> cfg=ft_definetrial(cfg); % to create all needed fields additionally to trl
> cfg.demean='yes';
> cfg.baselinewindow=[-0.2,0];
> cfg.trl = trl;
> cfg.channel = {'MEG'};
> BLC =ft_preprocessing(cfg);
>
> cfg.layout='4D248.lay';
> cfg.channel = {BLC.label{1:10:end}};
> cfgbo=ft_databrowser(cfg,BLC);
>
> and I get the following error:
>
> ??? Attempt to reference field of non-structure array.
> Error in ==>  ft_databrowser at 411
>    eventtypes = unique({event.type});
>
> What do I do wrong?
>
> a similar error occure when I call in this way as well:
> cfgc            = [];
> cfgc.method='pca';
> cfgc.numcomponent=20;
> comp = ft_componentanalysis(cfgc, BLC);
>
> cfgb=[];
> cfgb.layout='4D248.lay';
> cfgb.channel = {comp.label{1:5}};
> %cfgb.ploteventlabels  ='colorvalue' ;%(default = 'type=value');
> cfgbo=ft_databrowser(cfgb,comp);
>
>
> Thanks
> Inbal
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> ------------------------------
>
> Message: 2
> Date: Sun, 20 May 2012 13:25:52 +0200
> From: Nathan Weisz<nathanweisz at mac.com>
> To: Email discussion list for the FieldTrip project
> 	<fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Changing samplingrate for EGI-data
> Message-ID:<FC2347C8-148B-48F6-8064-0EF0487104B8 at mac.com>
> Content-Type: text/plain; CHARSET=US-ASCII
>
> Hi Daria,
>
> 1. you may want to check out the EGI software. there should be some resampling tool. the you can read the downsampled data into FT.
> 2. you can read chunks of trials using ft_preprocessing. resample. at the end concatenate them with ft_appenddata
>
> ciao,
> n
>
> On 19.05.2012, at 20:58, Ingrid Nieuwenhuis wrote:
>
>> Hi Daria,
>>
>> Although the name of the ft_preprocessing function may have you suspect differently,with this function you can just 'read in' your data (given your computer has enough memory to contain the whole data) with out any extra preprocessing. Subsequently you can then just resample your data with, indeed, ft_resampledata. For the ins and outs of the ft_preprocessing function, I recommend you take a look at the FieldTrip wiki (fieldrtip.fcdonders.nl) and the preprocessing - reading continuous data tutorial (http://fieldtrip.fcdonders.nl/tutorial/continuous) in particular.
>>
>> Hope this helps,
>> Ingrid
>>
>> On May 19, 2012, at 8:21, Daria Laptinskaya<daria.laptinskaya at googlemail.com>  wrote:
>>
>>> Dear All,
>>>
>>> I wish to subsample my EGI-data from 1000 to 250 Hz before
>>> preprocessing to speed up the whole analysis.
>>> For the step descriped at
>>> http://fieldtrip.googlecode.com/svn/trunk/ft_resampledata.m the
>>> structure as obtained from the FT_PREPROCESSING function is needed.
>>> Does anyone have an idea for read the data with a changing
>>> samplingrate before preprocessing?
>>> It would really help me a lot!
>>>
>>> Thanks,
>>> Daria
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>
> ------------------------------
>
> Message: 3
> Date: Mon, 21 May 2012 09:18:59 +0200 (CEST)
> From: "Stolk, A."<a.stolk at fcdonders.ru.nl>
> To: Email discussion list for the FieldTrip project
> 	<fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] equal number of trials across conditions
> Message-ID:
> 	<96701170.281413.1337584739634.JavaMail.root at sculptor.zimbra.ru.nl>
> Content-Type: text/plain; charset=utf-8
>
> Hi Vitoria,
>
> With 'randperm' you can randomly select a number of trials from one set. If you think order is important, for example indicated by the the trialnumber, have a look at ft_stratify and method 'histogram'.
>
> I would perform these randomization steps after regular cleaning. Perhaps someone else has more fine-grained idea for your desired approach.
>
> Yours,
> Arjen
>
>
>
> ----- Oorspronkelijk bericht -----
>> Van: "Vit?ria Magalh?es Piai"<vitoria.piai at gmail.com>
>> Aan: fieldtrip at donders.ru.nl
>> Verzonden: Zondag 20 mei 2012 11:53:58
>> Onderwerp: [FieldTrip] equal number of trials across conditions
>> Hi everyone,
>>
>> I'm working on a dataset (ERPs, but this is not that relevant for the
>> question, I believe) for which one condition elicited more errors than
>> the other.
>>
>> I'd like to have both conditions with the same number of trials in the
>> analyses.
>> Ideally, I'd throw away the noisiest trials from one condition,
>> instead
>> of just start throwing away trials at random.
>>
>> I was thinking of using z-scores for that but I was wondering if any
>> of
>> you has already done this before and how. What would be the best way
>> to go?
>> Take the mean amplitude across all trials (collapsed over condition or
>> not?) and calculate the z-score for each trial individually? Then take
>> out the one with the largest scores? How does this approach sound?
>> Does FT keep information about the variance for each trial somewhere
>> in
>> the output of an artefact rejection function? Or would I have to
>> compute
>> that myself?
>>
>> I'd appreciate any suggestions or feedback.
>>
>> Cheers, Vit?ria
>>
>>
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>
> ------------------------------
>
> Message: 4
> Date: Mon, 21 May 2012 11:19:12 +0200
> From: Gio Piantoni<g.piantoni at nin.knaw.nl>
> To: Email discussion list for the FieldTrip project
> 	<fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] equal number of trials across conditions
> Message-ID:
> 	<CAHeOcru=82toczPcvmMYLVjdo-DoJPS-bw5ZqWmxDxJkjbnjDQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Vit?ria,
>
> I like the intuitive appeal of your approach, in order to keep only
> the "most representative" trials. However, I'd have serious concerns
> that your approach might not be valid.
>
> If you reject only the noisiest trials from condition A, you're
> applying a sort of extra preprocessing step to your data and this
> makes the comparison between conditions A and B not very meaningful.
> You cannot unequivocally attribute the difference between A and B to a
> real difference between experimental conditions or to the extra
> preprocessing step.
> More critically, if you only reject noisy trials in condition A,
> you'll systematically introduce heteroscedasticity in your data; this
> is against one of the assumptions of parametric testing.
>
> I agree with Arjen to use random sampling of the trials of condition
> A. Depending on what you want to do next, you can even get standard
> errors from this randomization, similarly to the bootstrap approach. I
> find this a very elegant way to deal with very unequal numbers of
> trials.
>
> Hope this helps,
>
> Best,
>
> Gio
>
>
> -- 
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